Featured Research

from universities, journals, and other organizations

New genetic method developed to pinpoint individuals' geographic origin

Date:

May 24, 2012

Source:

University of California - Los Angeles

Summary:

Scientists have developed an innovative approach for the modeling of genetic variation in two- or three-dimensional space called spatial ancestry analysis (SPA). With SPA, researchers model the spatial distribution of each genetic variant by assigning a genetic variant's frequency as a continuous function in geographic space.

Share This

SPA Genetic Mapping. Model-based mapping convergence with random initialization. Colors represent the true country of origin of the individual (also represented by country internet code). (a–d) A map generated by SPA. Iteration 1 starts with random positioning of individuals (a). By iteration 4, the northern and southern populations are separated (b). By iteration 7, the positioning of individuals is close to convergence (c). In iteration 10, individuals have reached their final positions (d). (e) A map generated by PCA9. (f) Map of Europe.

Understanding the genetic diversity within and between populations has important implications for studies of human disease and evolution. This includes identifying associations between genetic variants and disease, detecting genomic regions that have undergone positive selection and highlighting interesting aspects of human population history.

Related Articles

Now, a team of researchers from the UCLA Henry Samueli School of Engineering and Applied Science, UCLA's Department of Ecology and Evolutionary Biology and Israel's Tel Aviv University has developed an innovative approach to the study of genetic diversity called spatial ancestry analysis (SPA), which allows for the modeling of genetic variation in two- or three-dimensional space.

Their study is published online this week in the journal Nature Genetics.

With SPA, researchers can model the spatial distribution of each genetic variant by assigning a genetic variant's frequency as a continuous function in geographic space. By doing this, they show that the explicit modeling of the genetic variant frequency -- the proportion of individuals who carry a specific variant -- allows individuals to be localized on a world map on the basis of their genetic information alone.

"If we know from where each individual in our study originated, what we observe is that some variation is more common in one part of the world and less common in another part of the world," said Eleazar Eskin, an associate professor of computer science at UCLA Engineering. "How common these variants are in a specific location changes gradually as the location changes.

"In this study, we think of the frequency of variation as being defined by a specific location. This gives us a different way to think about populations, which are usually thought of as being discrete. Instead, we think about the variant frequencies changing in different locations. If you think about a person's ancestry, it is no longer about being from a specific population -- but instead, each person's ancestry is defined by the location they're from. Now ancestry is a continuum."

The team reports the development of a simple probabilistic model for the spatial structure of genetic variation, with which they model how the frequency of each genetic variant changes as a function of the location of the individual in geographic space (where the gene frequency is actually a function of the x and y coordinates of an individual on a map).

"If the location of an individual is unknown, our model can actually infer geographic origins for each individual using only their genetic data with surprising accuracy," said Wen-Yun Yang, a UCLA computer science graduate student.

"The model makes it possible to infer the geographic ancestry of an individual's parents, even if those parents differ in ancestry. Existing approaches falter when it comes to this task," said UCLA's John Novembre, an assistant professor in the department of ecology and evolution.

SPA is also able to model genetic variation on a globe.

"We are able to also show how to predict the spatial structure of worldwide populations," said Eskin, who also holds a joint appointment in the department of human genetics at the David Geffen School of Medicine at UCLA. "In just taking genetic information from populations from all over the world, we're able to reconstruct the topology of the global populations only from their genetic information."

Using the framework, SPA can also identify loci showing extreme patterns of spatial differentiation.

"These dramatic changes in the frequency of the variants potentially could be due to natural selection," Eskin said. "It could be that something in the environment is different in different locations. Let's say a mutation arose that has some advantageous property in a certain environment. So you can imagine then that a kind of force for genetic selection would make this mutation more common in that environment."

The research team began to examine all of the genes, and for each gene they computed how sharp of a change there was in the frequencies. They soon discovered that the genes which had the largest and most extreme changes are the ones that are known to have experienced selection in the recent past.

"So this is a new method for finding genes that are also undergoing selection in humans," Yang said.

University of California - Los Angeles. (2012, May 24). New genetic method developed to pinpoint individuals' geographic origin. ScienceDaily. Retrieved March 3, 2015 from www.sciencedaily.com/releases/2012/05/120524112531.htm

More Fossils & Ruins News

Featured Research

Mar. 2, 2015 — Richard III is the only male to be discovered at infamous former car-park site. A mysterious lead coffin found close to the site of Richard III's hastily dug grave at the Grey Friars friary has now ... full story

Mar. 1, 2015 — A study of how climate change has affected emperor penguins over the last 30,000 years found that only three populations may have survived during the last ice age, and that the Ross Sea in Antarctica ... full story

Feb. 27, 2015 — That swim tracks made by tetrapods occur in high numbers in deposits from the Early Triassic is well known. What is less clear is why the tracks are so abundant and well preserved. Paleontologists ... full story

Feb. 27, 2015 — DNA evidence shows surprise cultural connections between Britain and Europe 8,000 years ago. Researchers found evidence for a variety of wheat at a submerged archaeological site off the south coast ... full story

Feb. 26, 2015 — The miniweight boxing title of the animal world belongs to the mantis shrimp, a cigar-sized crustacean whose front claws can deliver an explosive 60-mile-per-hour blow akin to a bullet leaving the ... full story

Feb. 24, 2015 — Thirteen million years ago, as many as seven different species of crocodiles hunted in the swampy waters of what is now northeastern Peru, new research shows. This hyperdiverse assemblage, revealed ... full story

Feb. 24, 2015 — Tropical turtle fossils discovered in Wyoming reveal that when Earth got warmer, prehistoric turtles headed north. But if today's turtles try the same technique to cope with warming habitats, they ... full story

Feb. 24, 2015 — A French-Kenyan research team has just described a new fossil ancestor of today's hippo family. This discovery bridges a gap in the fossil record separating these animals from their closest ... full story

Feb. 24, 2015 — Climate-driven plague outbreaks in Asia were repeatedly transmitted over several centuries into southern European harbors, an international team of researchers has found. This finding contrasts the ... full story

Feb. 23, 2015 — New work on echinoids -- marine animals like sea urchins and sand dollars -- gives scientists a reason to rethink a classical pattern of evolution. Fossil-based studies have traditionally indicated ... full story

Related Stories

Dec. 18, 2014 — The United States is a melting pot of different racial and ethnic groups, but it has not been clear how the genetic ancestry of these populations varies across different geographic regions. In a ... full story

June 10, 2014 — A genetic analysis of DNA samples of approximately 3,700 Mexican and U.S. Latino individuals identified a gene variant that was associated with a 5-fold increase in the prevalence of type 2 diabetes, ... full story

Aug. 31, 2010 — Although the whole population can benefit from a physically active lifestyle, in part through reduced obesity risk, a new study shows that individuals with a genetic predisposition to obesity can ... full story

ScienceDaily features breaking news and videos about the latest discoveries in health, technology, the environment, and more -- from major news services and leading universities, scientific journals, and research organizations.